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AllelicImbalance (version 1.6.2)

Investigates allele specific expression

Description

Provides a framework for allelic specific expression investigation using RNA-seq data.

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Version

Version

1.6.2

License

GPL-3

Issues

0

Pull Requests

0

Stars

1

Forks

0

Maintainer

Jesper R Gadin

Last Published

February 15th, 2017

Functions in AllelicImbalance (1.6.2)

ASEset-class

ASEset objects
ASEset.sim

ASEset.sim object
ASEset-gbarplot

gbarplot ASEset objects
ASEset-scanForHeterozygotes

scanForHeterozygotes
ASEsetFromBam

ASEset from bam file
annotationBarplot

add annotation to AllelicImbalance barplot
ASEset-barplot

barplot ASEset objects
ASEset-glocationplot

glocationplot ASEset objects
AllelicImbalance-package

A package meant to provide all basic functions for high-throughput allele specific expression analysis
ASEset-gviztrack

ASEset-gviztrack ASEset objects
cigar-utilities

realCigarPosition
boxplot

boxplots
countAllelesFromBam

alleleCounts from bam file
chisq.test

chi-square test
binom.test

binomial test
barplot-lattice-support

lattice barplot inner functions for ASEset objects
decorateWithGenes

decorateWithGenes
defaultMapBias

Generate default mapbias from genotype
coverageMatrixListFromGAL

coverage matrix of GAlignmentsList
decorateWithExons

decorateWithExons
DetectedAI-class

DetectedAI class
genofilters

genotype filter methods
fractionPlotDf

Plot Dataframe
defaultPhase

defaultPhase
getAlleleCounts

snp count data
getSnpIdFromLocation

Get rsIDs from locations of SNP
gba

global analysis wrapper
detectAI

detectAI
getDefaultMapBiasExpMean

Map Bias
getAreaFromGeneNames

Get Gene Area
import-bam-2

Import Bam-2
import-bcf

Import Bcf Selection
import-bam

Import Bam
GRvariants

GRvariants object
implodeList.old

implode list of arguments into environment
inferGenotypes

infererence of genotypes from ASEset count data
GlobalAnalysis-class

GlobalAnalysis class
histplot

histogram plots
inferAltAllele

inferAltAllele
inferAlleles

inference of SNPs of ASEset
phaseArray2Matrix

phaseArray2Matrix
phaseMatrix2Array

phaseMatrix2Array
initialize-DetectedAI

Initialize DetectedAI
makeMaskedFasta

makes masked fasta reference
initialize-ReferenceBias

Initialize ReferenceBias
initialize-ASEset

Initialize ASEset
legendBarplot

add legend to AllelicImbalance barplot
ASEset-locationplot

locationplot ASEset objects
mapBiasRef

mapBias for reference allele
initialize-GlobalAnalysis

Initialize GlobalAnalysis
reads

reads object
randomRef

Random ref allele from genotype
regionSummary

regionSummary
refAllele

Reference allele
ReferenceBias-class

ReferenceBias class
scanForHeterozygotes.old

scanForHeterozygotes-old
ReferenceBias-show

genotype filter methods
refFraction

reference fraction